Gap43 (growth associated protein 43) - Rat Genome Database

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Gene: Gap43 (growth associated protein 43) Rattus norvegicus
Analyze
Symbol: Gap43
Name: growth associated protein 43
RGD ID: 62071
Description: Exhibits lysophosphatidic acid binding activity; phosphatidylinositol phosphate binding activity; and phosphatidylserine binding activity. Involved in nervous system development; regulation of postsynaptic specialization assembly; and tissue regeneration. Localizes to GABA-ergic synapse and cytoplasm. Biomarker of visual epilepsy. Orthologous to human GAP43 (growth associated protein 43); PARTICIPATES IN N-cadherin signaling pathway; INTERACTS WITH (+)-pilocarpine; (S)-amphetamine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: axonal membrane protein GAP-43; Basp2; brain abundant membrane attached signal protein 2; brain abundant, membrane attached signal protein 2; growth accentuating protein 43; growth-associated protein 43; MGC156666; neuromodulin; protein F1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21158,376,371 - 58,470,047 (+)NCBI
Rnor_6.0 Ensembl1158,624,198 - 58,717,914 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01158,624,198 - 58,717,916 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01162,777,623 - 62,870,998 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41159,989,085 - 60,083,971 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11160,046,673 - 60,141,558 (+)NCBI
Celera1157,921,205 - 58,014,789 (+)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP,ISO)
(S)-amphetamine  (EXP)
(S)-nicotine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3-methyladenine  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-(1,4-diazepane-1-sulfonyl)isoquinoline  (EXP)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrylamide  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-D-galactose  (ISO)
ammonium chloride  (EXP)
arachidonic acid  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (ISO)
atrazine  (ISO)
azamethiphos  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP)
Brodifacoum  (EXP)
butan-1-ol  (EXP)
cadmium atom  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
carvedilol  (EXP)
chlorpyrifos  (EXP)
clobetasol  (ISO)
clorgyline  (EXP)
cobalt dichloride  (EXP)
cocaine  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (EXP)
cyfluthrin  (ISO)
cyhalothrin  (EXP)
cypermethrin  (ISO)
cytarabine  (ISO)
decabromodiphenyl ether  (EXP,ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibenz[a,h]anthracene  (ISO)
dieldrin  (EXP)
dioxygen  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
fasudil hydrochloride  (EXP)
fenvalerate  (EXP)
fluoxetine  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
galactose  (ISO)
glyphosate  (ISO)
Goe 6976  (ISO)
heptachlor  (EXP)
imipramine  (EXP)
isophthalic acid  (ISO)
kainic acid  (EXP)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
lovastatin  (ISO)
Meclizine  (ISO)
megestrol  (ISO)
melatonin  (EXP)
melittin  (ISO)
menadione  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
Methazolamide  (ISO)
Mipafox  (ISO)
N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2-ylidene)acetamide  (ISO)
N-acetyl-L-cysteine  (EXP)
nickel atom  (EXP)
nicotine  (ISO)
Oxadiazon  (ISO)
panobinostat  (ISO)
paraoxon  (ISO)
paraquat  (EXP)
pentobarbital  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phencyclidine  (EXP)
PhIP  (EXP)
potassium chloride  (EXP)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
Salinomycin  (ISO)
sarin  (ISO)
SB 431542  (ISO)
scopolamine  (ISO)
sodium arsenite  (EXP,ISO)
sulindac  (ISO)
Testosterone propionate  (EXP)
thapsigargin  (ISO)
thyroxine  (EXP)
titanium dioxide  (ISO)
trichlorfon  (ISO)
trichostatin A  (ISO)
tris(2-chloroethyl) phosphate  (EXP)
Tryptanthrine  (ISO)
tunicamycin  (ISO)
undecane  (EXP)
valproic acid  (ISO)
verapamil  (ISO)
vorinostat  (ISO)
zearalenone  (EXP)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bartolome MV, etal., Histol Histopathol 2002 Jan;17(1):83-95.
2. Boczek T, etal., Mol Cell Biochem. 2012 Jan;360(1-2):89-102. doi: 10.1007/s11010-011-1047-3. Epub 2011 Sep 13.
3. Dominguez-Gonzalez I, etal., Biochem J. 2007 May 15;404(1):31-43.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Houbre D, etal., J Biol Chem. 1991 Apr 15;266(11):7121-31.
7. Irwin N, etal., Proc Natl Acad Sci U S A 2002 Sep 17;99(19):12427-31.
8. Karns LR, etal., Science 1987 May 1;236(4801):597-600.
9. Kesterson KL, etal., Brain Res Dev Brain Res 2002 Dec 15;139(2):167-74.
10. Martins F, etal., Sci Rep. 2018 Feb 23;8(1):3548. doi: 10.1038/s41598-018-21453-3.
11. McNamara RK and Lenox RH, J Neurosci Res. 2000 Nov 1;62(3):416-26.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Nedivi E, etal., J Neurosci 1992 Mar;12(3):691-704.
15. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Tsuzuki K, etal., Acta Otolaryngol 2002 Mar;122(2):161-7.
20. Uittenbogaard M, etal., J Neurochem 2003 Feb;84(4):678-88.
21. Urdzíková LM, etal., Int J Mol Sci. 2014 Jun 25;15(7):11275-93. doi: 10.3390/ijms150711275.
22. Verze L, etal., Ann Anat 2003 Jan;185(1):35-44.
23. Wang CY, etal., Mol Cell Biol. 2015 May;35(10):1712-26. doi: 10.1128/MCB.01332-14. Epub 2015 Mar 9.
24. Young E, etal., Hippocampus 2002;12(4):457-64.
Additional References at PubMed
PMID:1533624   PMID:3428269   PMID:3581170   PMID:7859286   PMID:8694767   PMID:8889548   PMID:10482234   PMID:10662636   PMID:10850491   PMID:11703425   PMID:11839359   PMID:12034726  
PMID:12105219   PMID:12106089   PMID:12210137   PMID:12477932   PMID:12485886   PMID:12631465   PMID:12701761   PMID:12814368   PMID:14519521   PMID:14559368   PMID:14598294   PMID:14637107  
PMID:14648693   PMID:14978216   PMID:15052664   PMID:15071120   PMID:15182364   PMID:15234344   PMID:15246990   PMID:15502978   PMID:15964096   PMID:16269460   PMID:16330713   PMID:16820009  
PMID:16892058   PMID:17114649   PMID:17146769   PMID:17287580   PMID:17601561   PMID:17845802   PMID:18019391   PMID:18184180   PMID:18455509   PMID:18502309   PMID:18724891   PMID:19235891  
PMID:19249369   PMID:19443652   PMID:19761692   PMID:19782125   PMID:19805073   PMID:20035832   PMID:20090303   PMID:20173666   PMID:20335141   PMID:20406666   PMID:20423852   PMID:20646586  
PMID:20667480   PMID:21046809   PMID:21137370   PMID:21167390   PMID:21210085   PMID:21436126   PMID:21671799   PMID:21687946   PMID:21695168   PMID:21723373   PMID:21752992   PMID:21821100  
PMID:21822733   PMID:21868332   PMID:21948316   PMID:22063813   PMID:22121776   PMID:22490962   PMID:22617637   PMID:22871113   PMID:23119112   PMID:23316631   PMID:23426659   PMID:23586486  
PMID:23666783   PMID:23938193   PMID:24023391   PMID:24244461   PMID:24350898   PMID:24458787   PMID:24567055   PMID:24582971   PMID:24665937   PMID:25165142   PMID:25686598   PMID:25868328  
PMID:26238991   PMID:26503622   PMID:26850084   PMID:26865625   PMID:27412933   PMID:28801169   PMID:28871047   PMID:29286154   PMID:29486290   PMID:30682386   PMID:30911273   PMID:32095982  


Genomics

Comparative Map Data
Gap43
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21158,376,371 - 58,470,047 (+)NCBI
Rnor_6.0 Ensembl1158,624,198 - 58,717,914 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01158,624,198 - 58,717,916 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01162,777,623 - 62,870,998 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41159,989,085 - 60,083,971 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11160,046,673 - 60,141,558 (+)NCBI
Celera1157,921,205 - 58,014,789 (+)NCBICelera
Cytogenetic Map11q21NCBI
GAP43
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3115,623,510 - 115,721,490 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl3115,623,324 - 115,721,490 (+)EnsemblGRCh38hg38GRCh38
GRCh383115,623,510 - 115,721,485 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373115,342,357 - 115,440,330 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363116,825,142 - 116,922,842 (+)NCBINCBI36hg18NCBI36
Build 343116,825,141 - 116,922,842NCBI
Celera3113,750,041 - 113,848,417 (+)NCBI
Cytogenetic Map3q13.31NCBI
HuRef3112,715,632 - 112,815,889 (+)NCBIHuRef
CHM1_13115,305,939 - 115,404,101 (+)NCBICHM1_1
Gap43
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391642,068,915 - 42,161,014 (-)NCBIGRCm39mm39
GRCm39 Ensembl1642,068,805 - 42,161,014 (-)Ensembl
GRCm381642,248,552 - 42,340,651 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1642,248,442 - 42,340,651 (-)EnsemblGRCm38mm10GRCm38
MGSCv371642,248,665 - 42,340,764 (-)NCBIGRCm37mm9NCBIm37
MGSCv361642,167,884 - 42,259,983 (-)NCBImm8
Celera1642,611,179 - 42,699,387 (-)NCBICelera
Cytogenetic Map16B4NCBI
cM Map1628.37NCBI
Gap43
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542715,695,963 - 15,791,327 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542715,696,549 - 15,791,279 (+)NCBIChiLan1.0ChiLan1.0
GAP43
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13119,682,743 - 119,780,290 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3119,734,942 - 119,780,290 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03112,765,576 - 112,863,118 (+)NCBIMhudiblu_PPA_v0panPan3
GAP43
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13319,668,491 - 19,770,509 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3319,656,835 - 19,770,408 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3319,775,530 - 19,877,471 (+)NCBI
ROS_Cfam_1.03319,917,865 - 20,017,414 (+)NCBI
UMICH_Zoey_3.13319,722,015 - 19,823,783 (+)NCBI
UNSW_CanFamBas_1.03319,768,803 - 19,870,740 (+)NCBI
UU_Cfam_GSD_1.03320,313,727 - 20,415,899 (+)NCBI
Gap43
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602134,430,958 - 134,526,139 (-)NCBI
SpeTri2.0NW_0049365362,995,654 - 3,091,079 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GAP43
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13144,364,314 - 144,855,433 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113144,364,314 - 144,458,136 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213153,842,841 - 153,937,719 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GAP43
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12265,142,472 - 65,242,185 (-)NCBI
ChlSab1.1 Ensembl2265,142,039 - 65,242,222 (-)Ensembl
Gap43
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473132,629,586 - 32,748,515 (-)NCBI

Position Markers
GAP43  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21158,469,543 - 58,469,694 (+)MAPPER
Rnor_6.01158,717,413 - 58,717,563NCBIRnor6.0
Rnor_5.01162,870,495 - 62,870,645UniSTSRnor5.0
RGSC_v3.41160,083,468 - 60,083,618UniSTSRGSC3.4
Celera1158,014,286 - 58,014,436UniSTS
Cytogenetic Map11q21UniSTS
PMC17794P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21158,424,505 - 58,424,670 (+)MAPPER
Rnor_6.01158,672,417 - 58,672,581NCBIRnor6.0
Rnor_5.01162,825,652 - 62,825,816UniSTSRnor5.0
RGSC_v3.41160,037,625 - 60,037,789UniSTSRGSC3.4
Celera1157,969,327 - 57,969,491UniSTS
Cytogenetic Map11q21UniSTS
AU048143  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21158,448,030 - 58,448,184 (+)MAPPER
Rnor_6.01158,695,940 - 58,696,093NCBIRnor6.0
Rnor_5.01162,849,175 - 62,849,328UniSTSRnor5.0
RGSC_v3.41160,062,186 - 60,062,339UniSTSRGSC3.4
Celera1157,992,815 - 57,992,968UniSTS
Cytogenetic Map11q21UniSTS
UniSTS:265709  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21158,469,428 - 58,469,776 (+)MAPPER
Rnor_6.01158,717,298 - 58,717,645NCBIRnor6.0
Rnor_5.01162,870,380 - 62,870,727UniSTSRnor5.0
RGSC_v3.41160,083,353 - 60,083,700UniSTSRGSC3.4
Celera1158,014,171 - 58,014,518UniSTS
Cytogenetic Map11q21UniSTS
PMC337033P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21158,469,539 - 58,469,694 (+)MAPPER
Rnor_6.01158,717,409 - 58,717,563NCBIRnor6.0
Rnor_5.01162,870,491 - 62,870,645UniSTSRnor5.0
RGSC_v3.41160,083,464 - 60,083,618UniSTSRGSC3.4
Celera1158,014,282 - 58,014,436UniSTS
Cytogenetic Map11q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)114444434769649708Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:77
Interacting mature miRNAs:96
Transcripts:ENSRNOT00000002091
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 23
Medium 1 2 51 22
Low 2 40 17 8 2 8 8 11 21 13 8 8
Below cutoff 1 25 18 17 18 14 5 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002091   ⟹   ENSRNOP00000002091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1158,624,198 - 58,717,914 (+)Ensembl
RefSeq Acc Id: NM_017195   ⟹   NP_058891
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21158,376,371 - 58,470,047 (+)NCBI
Rnor_6.01158,624,198 - 58,717,916 (+)NCBI
Rnor_5.01162,777,623 - 62,870,998 (+)NCBI
RGSC_v3.41159,989,085 - 60,083,971 (+)RGD
Celera1157,921,205 - 58,014,789 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058891   ⟸   NM_017195
- UniProtKB: P07936 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002091   ⟸   ENSRNOT00000002091
Protein Domains
IQ

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698129
Promoter ID:EPDNEW_R8654
Type:single initiation site
Name:Gap43_1
Description:growth associated protein 43
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01158,624,291 - 58,624,351EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62071 AgrOrtholog
Ensembl Genes ENSRNOG00000001528 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002091 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002091 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:8364847 IMAGE-MGC_LOAD
InterPro IQ_motif_EF-hand-BS UniProtKB/Swiss-Prot
  Neuromodulin UniProtKB/Swiss-Prot
  Neuromodulin_C UniProtKB/Swiss-Prot
  Neuromodulin_gap-junction_N UniProtKB/Swiss-Prot
  Neuromodulin_P_site UniProtKB/Swiss-Prot
  Neuromodulin_palmitoyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29423 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156666 IMAGE-MGC_LOAD
NCBI Gene 29423 ENTREZGENE
Pfam Neuromodulin UniProtKB/Swiss-Prot
  Neuromodulin_N UniProtKB/Swiss-Prot
  PF00612 UniProtKB/Swiss-Prot
PhenoGen Gap43 PhenoGen
PRINTS NEUROMODULIN UniProtKB/Swiss-Prot
PROSITE NEUROMODULIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NEUROMODULIN_2 UniProtKB/Swiss-Prot
  PS50096 UniProtKB/Swiss-Prot
SMART SM00015 UniProtKB/Swiss-Prot
UniProt NEUM_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q63212_RAT UniProtKB/TrEMBL
UniProt Secondary A0JPM4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Gap43  growth associated protein 43      Symbol and Name updated 629477 APPROVED
2003-03-14 Gap43  growth associated protein 43  Basp2  brain abundant, membrane attached signal protein 2  Data Merged 628472 PROVISIONAL
2002-08-07 Basp2  brain abundant, membrane attached signal protein 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Gap43  growth associated protein 43      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process mediates axon growth and synaptic plasticity 625586
gene_regulation mRNA increased by nerve growth factor (NGF) due to the ARPP-19 dependent increase of mRNA half-life 625586